Whispers of the Wolf
by TwilightLabyrinth
Summary: On an adventure with the Ponds the Doctor discovers an old friend in bad shape. But what happened to her? Who put her in the asylum? And more importantly, what does she know about the Doctor's future? Rosex11 and AmyxRory. Set mainly before Rebel Flesh and The Almost People and then around A Good Man Goes to War.
1. Forever

"Security, breach on level 700. All units report to Holding Chamber One, repeat all units report to holding chamber one." The automated voice rang out over the intercom.

The Doctor led the Ponds through the labyrinth of hallways. Something was not right. The asylum on Delta 79 was known for it's care and astounding recovery rate but he had never thought that the bright exterior might have hidden something sinister. Taking out his sonic he hacked an interface n the wall hoping to locate Holding Chamber One. Whatever the asylum was hiding he was sure it was in there. It took him back to New Earth and the trip he took with Rose to the 15th New York. Oh, he hoped it wasn't like that. Finally find the proper path he turned back and started back.

"Come on Ponds!" he called.

"Wait! Doctor, what's in Holding Chamber One?" Amy asked.

"No clue. That's the fun part." He said with a smile.

Amy threw a side glance back at her husband but ran to catch up anyway. By the time the reached the outer doors of the chamber the security divisions were gone. The Doctor began scanning the first set of doors in an attempt to open them. After a moment they slid apart revealing a control room of sorts that the Doctor brushed off. A sinking feeling was forming in his gut. From what he could tell from a brief glance at a monitor there was only one person in the room lying on the bed unconscious. He moved to the second set of doors. Unlike the first he could see directly into the chamber. The view didn't allow him to see the room's occupant but he could see the walls. Both his hearts stopped as he tried to force the doors open.

"Doctor, what's wrong?" Rory asked.

"No, no, no, no, NO!" The Doctor yelled.

Finally the doors slipped open and the Doctor rushed inside. The occupant remained slightly lifeless on the bed. Kneeling by the bedside the Doctor gathered the woman into his arms and brushed the hair from her face. They had sedated her. The had locked her up here and...done things to her, to her mind. And he had let them. Oh, god, he had let them. He held her and rocked her back and forth gently. He heard his companions come in behind him. They both paused a moment to look at the walls. Their eyes drifted upwards.

"Doctor..." Amy started but couldn't find the words.

"According to the files, her name is Rose Tyler. She was brought here and diagnosed with the Bad Wolf Virus." Rory took a closer look at the writing on the walls. "Oh my god, is that...blood?"

The Doctor put Rose back onto the lumpy bed gently careful not to hurt her on accident. When he was sure she was comfortable, he joined the couple. Taking out his sonic again he scanned the writing. Sure, enough it was blood, Rose's blood. He felt ill. Looking up he tried to make sense of it all. _Bad Wolf. Doctor. The Bad Wolf will swallow the Universe._ _Round and round it goes, it never stops. It won't let me go. I need my Doctor. Save me._ The words were everywhere. Pleas for help, prophecies, all coming from the depths of her broken mind. Smaller and lower to the ground there was a phrase that she'd only written once. The neatness of the script spoke to what had remained of her sanity at that point._ The Storm and the Wolf, the stuff of Legends. _His hearts broke. He understood now, partially at least.

"It was for her own good, Doctor. Don't you see? The Wolf threatened to consume her, she needed our help." one of the compound's doctors stood in the doorway watching the Timelord with interest.

"No, because you only made it worse." the Doctor said turning sharply. "Now it has consumed her." He pointed the sonic at the smaller alien. "Now you'd better run because now the Storm is here and he is ready to let his Wolf go."

The alien man ran from the room. It took the Doctor a moment to lower his arm but the anger he'd shown never left his face. Ignoring the Ponds he gently gathered the woman into his arms and began to carry her to the TARDIS. He could hear the couple behind him calling out, trying to catch up to him but his mind was beyond explaining to them now. Right now he needed to get Rose to the TARDIS without succumbing to the desire to destroy the entire planet for what they'd done to her back there in that horrible room.

He looked down at her sleeping face. She hadn't aged a day since he'd last see her, not that he could bare to think of that either. Yet even in sleep her face was contorted in pain from nightmares he couldn't fight away for her. He wanted to help, wanted to make up for not finding her sooner, for not ripping the worlds apart like he'd wanted to and taking her back. Not matter what, he vowed, he wouldn't let any of that happen again. As long as he was alive, Rose Tyler would be safe.

"Doctor!" Amy yelled.

"Not now, Pond. We need to get her back to the TARDIS." the Doctor said.

Signing in defeat the redhead followed him in to the TARDIS. The Doctor laid the woman down on the floor and tried to arrange her in a comfortable manner before he ran to the console to try to do some scans or something. Seeing the blonde girl shiver Amy ran off to fetch a blanket. Upon returning she noticed that not only was she shivering but her face and neck were covered in a light sheen of sweat. Amy looked up at the Doctor. He was obviously engrossed in whatever it was he was doing. So Amy took it on her self to check on her. Gently she slid her hand on to Rose's forehead.

"Anything?" Rory asked coming up behind his wife.

"She's burning up."

Rory checked. "I was reading her file. I think that doctor was right. Whatever it is it's consuming her, quite literally burning her from the inside out. His name was written all over those walls. Even River's little poem was on that wall. It was like she knew. But she'd been locked up for years."

"Rory's right. She did know, she knows about all of it. That's half the reason she's like this." The Doctor said.

The alien time traveler had reappeared in front of the three of them. For a moment Amy thought of asking again just who this woman was but then she noticed the look in his eyes. She imagined it had been there before when he'd first found her. She had seen him hold her in his arms like he was praying to whatever it is Timelords prayed to that she was alright. Now it seemed like there was a tint of guilt mixed in with his worry. There was a beep from the console. The poor man stood slowly and checked the monitor. The tension in his back relaxed a little bit.

Smiling in their direction he sighed. "As I thought, just being in the TARDIS has stabilized her. If she makes it through tonight she'll be fine."

With one more sad twitch of his mouth he took her in his arms again and, presumably, carried her off to a room with a bed. He had no doubt that she would a have more violent outbursts and considering the care he'd put in to preserving her room in case the impossible happened and, she did return, he would hate for her to destroy her own prized possessions. So he made a turn down another hallway. There was only one room this way. His room. The TARDIS hummed gently as she slid the door open. An image flashed in his mind of dreams and visions of this being their room. Somehow he maneuvered it so she was in the center of the bed wrapped in several blanket without really letting her go.

She sighed and twisted in the makeshift cocoon. "I waited for you..." she mumbled. His hearts shattered. "The Storm and the Wolf...you said we were the stuff of legends."

"And you promised me forever, Rose Tyler." He whispered.


	2. Bad Wolf

The Doctor stayed with Rose all night. After she'd spoken out to him she'd slept soundly. Thanks to that he'd even managed to catch some sleep himself just on the edge of the bed. When he woke up he showered quickly and dressed. Amy was already waiting for him against the console. He wished he could explain to her what Rose meant to him, how she'd saved him in so many ways. She stayed with him as he ran a few more tests and scans in silence. The determined look painted on his face kept her silent but her Scottish fire couldn't be held off forever, even the Doctor knew that. Eventually she would just have to ask him about the truth.

"You never said who she was." Amy said.

It took the Doctor a moment to process the statement. "She's Rose Tyler."

"Not just her name. Who is she? How do you know her?" Amy asked.

He sighed. "She was a companion of mine long before I knew you. Those were...darker times. I was a much different man then. She was a lot like you. No matter where we went she looked at everything with wonder and always had a deep respect for the species we met. She showed me how to live again. Then, then she was taken from me. I had to leave her with a clone of myself. It's all rather complicated."

"You loved her and you left her with a clone." Amy couldn't believe what she'd just heard.

"It was complicated!" The Doctor cried. "I just...I just wanted her to be happy." He sighed and collapsed into the jump seat. "I wanted to give her the life I never could have with her and give her what she wanted with him. He was me, same memories, everything, only he had just one heart. He could live with her, have a family with her, die with her."

Amy walked over and bumped the Doctor aside a little. Her childhood friend smiled at her sadly. That was how Rory found them. The saddened Time Lord just sat there looking at the floor like there was something suddenly interesting about the transparent grating. When he looked at his wife she shook her head. The Last Centurion studied the two in silence. The Doctor had calmed since last night when he'd been threatening doctors and looking like he would kill anyone who got in his way. He took that to mean Rose Tyler had survived the night.

"Ummm, Doctor, I wanted to offer my help. I am a trained nurse. If you need any help..." Rory offered.

There was an ancient sadness in he's eyes when they met Rory's. "Thank you, Rory." the gratitude in his voice was undeniable. "Now let's get going."

The Doctor hopped up and headed toward the door. As far as his current companions were concerned they hadn't left the asylum. So where was he going? He looked back at them half way out the door. They shared a look before they ran to catch up to the mad man. Outside the TARDIS the asylum was moving at a relatively normal pace. Still each of the staff members moved away from them as the moved through the crowds. Amy looked at the shorter aliens with anger and a little bit of worry. They had done something to Rose to make her that way and she wasn't sure she trusted them. Still none of them tried to stop the three time travelers as they headed toward the holding cell where the asylum had been holding Rose.

"Doctor, what exactly are we doing here?" Amy asked.

"I need to see what exactly they were doing to her." the Doctor said using the screw driver to hack the computers.

A video started to play. Rose was thrown into the room but the person didn't step in after her. She turned and tried to run but was pushed back. Correction, she'd been punched. All three notice it at the same time, the moment she looked up at the camera and wiped some blood off her lip. The next three days of tape were calm and were sped up to save them time but then something happened. A nurse came in and gave Rose some kind of shot that left Rose in the middle of a horrible seizure. Her skin began to glow bright gold. Amy and Rory stared disbelieving and confused. The Doctor on the other hand felt a though he was watching a Time Lord regenerating. When the light faded Rose was fine, for the most part. This was where her madness had begun to set in. The forced regenerations happened everyday after that. It seemed that the doctors had no idea that someone else was causing it.

"What are they doing to her?" Amy asked.

"It's not them. It's someone else and their killing her and forcing her body to heal itself like a Time Lord's would. Except," the Doctor tried to chose his words carefully. "Except, her body isn't changing, just dying and coming back."

What came next was not unexpected but he rather wished it hadn't happened in the first place. Sharp nails dug into her arm drawing blood. Her fingers dipped in it she began to write her messages. Before he noticed it a hot tear was rolling down the Doctor's cheek. His poor, sweet Rose. He shouldn't have left her alone for so long. As soon as she was well he would take her where ever, when ever she wanted to go for the rest of eternity and he would tell her everything. She deserved to hear him finish that sentence and explain it like he'd wanted to that day when all three of them had stood together on that beach. He would break every one of his rules for her.

Rory fast-forwarded when he noticed the tears on the Doctor's cheeks. "Wait stop!" Amy yelled.

"Amy...he doesn't need..." Rory said.

"No, look. There, do you see that." She was pointing to something on the screen. "That wasn't there when we found her last night."

Rory rewound a little. Rose was in the corner writing in her own blood yet again. _They took her. They took my baby, my little R_...Suddenly the nurse who had been causing Rose pain came in and sedated her. By the time the doctors returned the incomplete message had been washed away. Instead of staying to watch the rest the Doctor went back to the TARDIS. Rose Tyler and his clone had a child. Or was that just one of the delusions caused by her illness? He had to find out.

After finishing the video the married couple returned to find the Doctor staring at the screen in the console room. "It wasn't a delusion. She had a baby. She had a life."

The look in his eyes was so broken even Rory felt like crying for him. He had gotten the gist of it from the Doctor's actions and realized a long time ago that he loved this Rose Tyler who ever she was and that seeing her like this had hurt him. But it was even worse knowing that the woman you love had a life with someone else. Thinking of it, of Amy with someone else, made Rory want to die inside. Knowing the Doctor, the alien had probably found a way to blame himself for all of it. Including the fact that Rose had lost that child in some way. And that child might be out there somewhere alone and in danger.

"What do we do now?" Amy asked.

"We wait. We go out on adventures and we wait."

The Doctor set off toward his room. When he saw Rose laying on his bed he started truly crying. Taking her hand he murmured apologies and rubbed circles on her hand with his thumb. For now she looks so calm, so serene, and he began to fear that she would fall back into what she had been in the videos. He wanted to save her. He wanted to give her back the life she'd had, even if it meant that he would have to be out of her life forever. He wold do it for her.

"I need you to stay strong for me, Rose. I'll fix this, I will save you, just please, give me time." He begged.

There were so many problems for him to handle at the moment. First there was Rose. Rose's mind was so far from her. All he think about was how he had driven her to it in someway or another. For leaving her, for sending her back, for not truly ridding her of the Bad Wolf. Then there was the Silence and their cult. Whatever they had been doing with that space suit he wasn't sure it was over. And finally there was Amy. For some reason his scanners were constantly contradicting themselves. He needed to find out what was really going on with her. So many problems and he was no closer to solving any of them than he was before he'd known about them.

"Please, Rose. I could really use your brilliant mind right about now." She made groaning sound. "I'm sorry?" she groaned again and he finally understood. He held a cup to her lips and helped her to drink the cool water.

She sighed. "...flesh..."

The Doctor jumped. "You are brilliant!"


	3. Demon's Run

The Doctor slipped into his room silently. Thanks to her hint he'd learned that there was a group holding the real, and very pregnant, Amy Pond. Now he and Rory were gathering allies and claiming old debts. What he wouldn't give to have Rose or the damned Wolf as an ally in this fight. Yet he would give anything to keep her safe at this time. He kissed her forehead and brushed a bit of golden hair from her face. She was so much stronger now. He could feel her mind now. It pushed at the walls of his mind but even when he lowered them it would not enter. Just like her it was waiting for him to make the first move. A smile slipped on to his lips. She hadn't really changed.

"I'm...I'm going to go now," Rory said dressed as the Last Centurion.

"Right," The Doctor said standing. Producing his sonic he handed it over to the man. "Take this."

The man took it with a nod. Once he was once again alone with Rose, the Doctor turned his mind back to his previous thoughts. Her walls were down, perhaps if he lowered his he might be able to fix her mind, manually piecing it back together until she was whole again. Taking a deep breath and lowering his walls, he felt her. Suddenly he felt cold, colder than he'd ever felt but he closed his eyes and braced himself this was her mind he had no idea what he would find. If this is how cold she really felt than he would have to find a way to fix that.

"Hello," a feminine voice said.

Realizing he'd had his eyes closed for a long time the Doctor jerked a little and opened them. "Hello."

Standing with her back to him not a few feet away was a very alive and very strong Rose Tyler. Besides that it took him a moment to realize exactly where they were. Darlig Ulv Straden, Bad Wolf Bay, no wonder it was so cold. Sea spray hit his face, cold and wet, why would she chose this place? Pain hit him when he realized exactly why this place was important enough be present in her mind. This was the last place they'd seen each other. He had refused to tell her the truth and had let his clone whisper it in her ear instead. He really hated himself for that. It was a mistake he would be paying for a long long time.

"Done with the guilt trip back there?" She asked.

He looked up. "Oi, cheeky!"

She giggled. The tongue in teeth smile she gave him made him want to jump her there and then. It distracted him from his train of thought for just a moment. "Wait, what's happening? How are you strong enough to do this?"

"My sweet Doctor, you've regenerated. You look so young now." She said she grabbed his face running her fingers over his cheek bones. She was distracting.

"Rose, please, tell me the truth."

"Did you think that my mind was truly that weak? Don't you know me better than that?" She stepped closer and brushed his hair into place.

"But the writing...a child...Rose, tell me the truth." Sad eyes met her's, pleading with her for some kind of answer.

She looked down. "I can't tell you everything. There are somethings you have to find out for yourself. But the writing, it was...I was trying to send you a message. Sometimes it was just blathering, I couldn't actually get my mind clear. Being on the TARDIS is helping with that." She met his eyes once more. "They were trying to make me do something. I'm not sure what but I know it didn't work. What I do know that they were trying to control the Bad Wolf."

"Rose...I saw the videos, the way you were acting...what was that? What happened?"

"The Bad Wolf...it's a part of me, like an animals instincts. They kept...they kept injecting me with something and...and it hurt." She was shaking now.

"Breath, Rose, I need you to breath."

His hands went to her face, thumbs brushed her cheek bones, fingers in her hair. She looked up at him again, this time her eyes flashed hazel to gold and back again. After taking a deep breath her eyes turned back to normal, the color he loved, the one he'd memorized and forced to remember as often as he could. It was one of the small things he could keep of her forever. Seeing her calm at last he wrapped his arms around her and just held her for a moment. She pushed him back a little.

Looking into his eyes she continued, "Whatever they did caused her to react constantly, we were fighting for control. After all of that it's my body that's weak, my mind, well take a look around."

He smiled. "But you are getting stronger."

"Yes, and you've been staying with me. Every night."

"I have." He said realizing now that she would have sensed him and felt him holding her and. "Yes, I...ahh...there's something I should tell you."

A soft finger appeared on his lips. "Shh...There's no rush. Tell me when I wake up. I'd rather look into your real eyes when we actually get to talk to each other."

"Rose, it's something that I should have said a long time ago."

"I figured. Still, I'd like to actually be standing with you, looking in your eyes when you tell me."

The idea that she knew exactly what he wanted to tell her made his hearts race. In the Pit he'd refused to say it and on the very beach where they now stood he'd been cut off but she knew and she was smiling and close. Mouth moving like a fish he tried his best to say something, anything, in response to her but came up short. He wanted to ask her if she still held to her last words to him. Did she still l...no he couldn't ask that. He couldn't think it. She was Rose Tyler, she was the best of the best, it didn't matter weather or not she loved him. She was alive and in her mind she wasn't angry about being left.

"Also, I'd like to be able to hug you. First time I'll have hugged the real you in this new body of yours." She smiled her signature tongue in teeth smile.

Seeing that smile brought back some of the best memories of them together. She was and would always be the brilliant and clever Rose Tyler. If had to classify her it would be as the one who came back, after all she'd done it three times now. Saved his life twice by doing so and now he prayed he'd get to return the favor. He held her close once again, even if this was just in their heads he didn't want to have to face the feeling of loosing her ever again. Not that she seemed to mind. Her head was pressed into the center of his chest, ear flat against him, listening. Most men would have found it sentimental and sappy but he knew that like him she needed to prove he was real and she was real and they were standing here together in the only way they could.

"So, what are you and the Roman up to?" she asked.

"Going to war, the Silence has Amy and her baby and we're going to get them back."

He felt her face drop and she mumbled something. "Be careful." She said finally.

He could tell she was holding back but he didn't push it. Under normal circumstances he should have understood what she'd said. He had no doubt that it was the Bad Wolf covering up its host's slip of the tongue. The Doctor rubbed her back gently careful not to push her past anything they'd done previously and anything that would compromise her relationship with his clone. No matter how much he wanted her he would never hurt her like that.

"I will." he whispered.

"I'd like to stay with you for a while longer but you need too go rescue her."

"Time moves differently here."

"I know. Still I'd like to get out and watch you work. It's one of the things I miss most about our travels." She said smiling again. "There is away."

"Oh, really, how's that?"

"I open a psychic link with the TARDIS and you open up a window for a holographic image. I'd be with you, sans touching. And doubt worry I won't disturb the guests...much."

"I think Jack rubbed off on you a little too much."

He nodded his ascent and pulled from her mind. Outside not a moment had passed but there was a beautiful smile painted on her lips. In the console room he did as she'd instructed and as the TARDIS advised. Within moments there was Rose standing in the TARDIS like nothing had changed, staring at the new design of the room. He held his breath, certain she would hate all the changes that had happened after she'd left. Then she turned and smiled. Damn, that smile would be the death of him. She ran passed him and sat in one of the two jump seats. The TARDIS made it swivel a little just to make it look like she was really there.

"So where to now?"

"London, 1888! hold on tight Rose Tyler!" the Doctor yelled.

Rose giggled holing back the desire to tell him to run, to play the coward and run. But she knew he wouldn't. If ever there was something that could get the Doctor to fight it was putting one of his companions in harm's way. Kovarian knew what she was doing. Rose just hoped the Doctor could remain calm, the Storm would be of no use to him at Demon's Run. In fact, it would prove to be his downfall. Just like Kovarian had said.


	4. A Good Man Goes to War part 1

"You will stay here, Amelia Pond, until the Doctor comes to fetch you." Madame Kovarian said as the soldiers pushed Amy into a room.

The room was stark white and blindingly bright consider the lack of obvious light sources. Amy forced herself to blink and adjust so she could take it all in. Across the room the room there was a window that looked out into a larger darker room. Besides that there was no physical proof that anything sinister was going on. Her hand wandered to her stomach. No physical proof at all. Looking back around the room she noticed there were toys scattered around the floor just like the little house in Florida. The same pictures were sitting on a low table near the bottom of the stairwell. Several of them featured to little girl all alone but one sported a young Rose and a baby. Amy wouldn't have noticed it before but now it was obvious, the girl was Rose's lost daughter.

"Hello?" a little girl's voice asked.

Amy turned to find the little girl holding tight to a stuffed bear. "Hello, I'm Amy. I'm a friend." She walked over to the girl slowly.

"I'm...I'm..."The girl started to cry. "I want to go home."

"Shhh...Don't worry. There are two very brave men out there. They're coming to save us. One of them has a time machine and as soon as it's safe he'll take you where ever or when ever you want. Ok?" The girl nodded through her tears.

"They...they took...they took my mum away."

"Shhh...it'll be ok, we'll find her." _Hurry up, Doctor. _"How about we play with those toys over there?"

The girl nodded wiping away her tears. She grabbed Amy's hand and pulled her to the small area. With out saying anything Amy could sense that it had been a long time since the girl had a play mate. Maybe not even since she'd been with her mother. They'd only been playing a few moments but Amy could tell that she'd managed to distract the girl from the problems they were facing. Now if she could only do the same for protecting her.

"So what's your name?" Amy inquired when she knew that the girl was completely happy.

Before the girl could answer one of the white walls slid open and Madame Kovarian entered. Rose's daughter grabbed on to Amy and she couldn't help one came next. There was danger in the air, tangible and heavy, Amy grabbed the girl and took her into her arms. She held her tight, maternal instincts kicking in. Glaring like a mother bear at the encroaching soldiers, she backed him into a corner. Right now Amy wanted to know why it was that they wanted the little girl. It was already obvious to her since they'd faked her pregnancy, kidnapped her, replaced her, that Amy was bait for the Doctor. They needed the Doctor and the little girl. _Anytime now. _

"Let her go, Amelia," Kovarian warned.

"No." Her stubbornness flared. She was not good at taking orders.

Sedate her." The order was sharp. There was no time for Amy to negotiate a peaceful surrender or an exchange. It suddenly became obvious to her. The girl was important, she on the other hand was expendable.

The last thing Amy would remember was kicking one of the soldiers down low and then a twinge of pain in her neck. Now she was waking up to the scared eyes of Rose's little girl. Despite her blurry eyes she could see the resemblance between the child and Rose but she noticed there was a bit of the Doctor in there, too. The girl must have gotten it from his clone. Also looking at her now Amy realized her age. The girl had to be almost four years old but she was able to communicate almost as well as the Doctor minus the rambling.

"I'm sorry," Amy gasped the sedative causing her words to slur.

"Amy, are they still coming to get you?" the little one asked.

"For us, they're coming for us." Amy said clearly.

"Amelia Pond get your coat we're going home!"Amy heard the doctor yell.

She and the little girl rushed to the window. Pressed against it she could just make out the shape of the Doctor below on a low platform. A small broke out across her face. In her excitement she almost missed the little girl's gasp. Amy turned in horror expecting the worst. Instead the girl was staring at where the Doctor had just been. The doors opened again and more soldiers entered. Once again grabbing the little girl Amy tried to make a break for it but was pushed back to the ground. Knowing anymore attempts would be foolish Amy covered the girl with her body and prayed to be able to wait them out and that somehow the Doctor would get there in time.

Unfortunately she wasn't strong enough. The girl screamed for her as the soldiers hauled her away and some stayed behind to hold her down. Feeling that the pressure on her back was no closer to lessening she took in the room as it was now. In the struggle the picture of Rose and her baby was on the floor glass broken but her beautiful smile remained. Somehow the image itself gave her hope. Rose was a fighter, she must have fought hard for the girl, that meant that the girl would be loved, even from a far, and she would know it. The soldier stepped ff her when she stopped fighting. She'd lost the little girl again.

Looking down into the cargo bay. The dark skinned soldier in charge was regaining control on the floor until the until the Doctor's voice came over loudly. Explosions began to wrack the ship but she couldn't help but smile. The Doctor was here in his usual fashion. When there was a knock at the door and Amy scrambled to grabbed something, anything, to fight off the on coming soldiers.

"Who's that? Who's there? Cause I am armed and really dangerous and cross." Amy said finding a medical tool of some kind.

"Yeah like I didn't already know that." Rory's voice muttered at the door.

"Rory? Rory is that you?"

"Yeah it's me." He was struggling with the lock. "Hang on a minute."

"Rory, there's something I have to tell you. They tricked us...I wasn't pregnant. They were just using me to get to him and it worked." Fresh tears burned at her eyes. "There was a little girl but they...they took her somewhere. We need to find her and get the Doctor before it's too late."

The doors opened. "Now Mrs. Williams, I think I found just the person you were looking for."

Rory stepped in carrying the little girl. The moment her eyes found Amy she was out of the centurions arms and down to her. "I am so sorry but now there are very good people here, here to save you."

"And you. They're here to save us both." the little girl said hugging Amy.

"Are you alright?" Rory asked. "I mean they..."

"I'm fine. They had me sedated, the contractions were fake, all they wanted was something to get the Doctor here for some reason. I was the bait."

Rory cupped his wife's face. "You are so much more than that." Then he kissed her.

"Ewwww...crying and kissing I think I'll come back later." The Doctor said with a twinge of guilt. Bait, for him.

"Oi, get down here now." The Centurion said.

The Doctor ran down the stairs to the two of them. "So, who is she?" he whispered.

Unable to respond properly Amy bent down and handed the Doctor the picture of Rose and her baby that had fallen. His response was an audible gasp and a rush of sadness to his eyes. Had this been what Rose refused to tell him? That her own daughter was on the asteroid and was being held by the Silence? Or was there more? He looked over at the little girl. How had anyone missed it? Her honey blond hair and brown eyes looked so much like her mother's it was startling.

"Hello," he said.

She stared back at him for a moment before rushing into his arms. By instinct he wrapped his arms around her and held her close. From the look in Amy's eyes this wasn't the way the girl would have responded earlier. Still he held her none the less reveling in the thought that the little girl might heal parts of Rose that he couldn't and that by returning her daughter he would be able to give back the life that the Silence had stolen from her.

"So little one, what is your nae?" he asked.

"Doctor! Take a look, they're leaving, Demon's Run is ours without a drop of blood split." Vastra said coming into the room. "My friend you have never risen higher."

Rory looked at the Doctor, River's words finally catching up to them. He held his wife a little bit closer. From what River'd said it was about to get extremely difficult. Together with the two girls Rory headed back to the TARDIS. Two minutes later Amy came running out with the little girl in her arms. Giving her a questioning look tinged with worry he asked her what was wrong. After settling her down, Amy managed to explain that the girl didn't like the noises the TARDIS was making so she'd brought them out here for now. As soon as all the others began to notice the little one's distress the attempted to give her aid. Even the Doctor tried to help. The girl just stared at him like he had to heads like she had before.

"Doctor, you need to see this." Vastra said over the speaker.

Entering the control room the Doctor was greeted by a sample of the girl's DNA. Dorium and Vastra tried to understand how it could be there believing the child was still Amy and Rory's. Seeing the mix of DNA on screen he felt ashamed. Rose's daughter was a Time Lady. Somehow despite the fact that her father was only half Time Lord the child had gotten all of it. Rose had to have already known that considering the two hearts. But it still begged the question, how? Unless...No, no, it wasn't possible.

_The young mother held her little bundle in her arms. Deeper brown eyes looked up at her hazel eyes with the undeniable love of a child for its mother. A small smile flitted across her lips. Standing the young mother walked over to the window to show her little daughter the night sky. Every night she dreamed of a blue box coming back for her. Since her daughter's birth she hadn't made it to work. Despite her desire to return and show him their child she didn't know how he'd react to the little girl in her arms. Just then the baby started to cry. _

"_Shhhh, my little River...shhhh its alright." the mother whispered._

_Leaning forward she began to sing. "Demons run when a good man goes to war._

_Night will fall and drown the sun,_ _When a good man goes to war._ _Friendship dies and true love lies,_ _Night will fall and the dark will rise,_ _When a good man goes to war._ _Demons run, but count the cost._ _The battle's won but the child is lost."_  
_The child was asleep before the song was done. A sad smile graced the mother's face as she laid her baby in her crib. For a moment the mother's eyes flashed a delicate golden color but as soon as she blinked her eyes returned to the normal hazel color. Kissing her baby's forehead she went back to the window to look at the stars and the planets swarming and circling above her head. She missed it, missed _him.  
**Everything must come to dust. All things, everything dies. **


	5. A Good Man Goes to War part 2

"The girl isn't Amy and Rory's." he said cutting one of them off. "Her mother's name was Rose and her father was half Time Lord. They took her and then they put Rose into an asylum to keep her out of the way and nearly killed her."

"That doesn't seem possible. But even if that clone of yours was her father there would be a trace of a second human in her DNA. There isn't." Dorium exclaimed upon reexamining it.

"Doctor, is it possible?" Vastra started to ask.

"Possible, what?"

The Silurian hissed and shook her head. "I'm trying to be delicate. I know how can you can blush? Is it possible that this clone of you isn't the father?"

Both of the Doctor's hearts stopped. "But that's impossible." he gulped thickly. "No, no that can't be possible. It was just one time. No, no, no. She would have told me!"

"They gave in too easily. Does this not bother anyone else?" Dorium asked.

"You can't just cook yourself a Time Lord." The Doctor argued.

"Of course not. You gave them one hell of a start. And they've been working very hard ever since."

"It's too easy. There's something wrong."

"Why do it? She's just a child! Even if she is...even if you could get your hands on a brand-new Time Lord, what for?"

"A weapon?" Vastra offered.

"Why would a Time Lord be a weapon?"

"Well," she and Dorium shared a look. "They've seen you."

"Me?"

"Mr. Maldovar, you're right-This was too easy. We should get back to the others."

The Doctor felt as though he would collapse then and there. The Silence saw him as a weapon and a threat and had stolen Rose's child, possibly his, to destroy him. All of this done to end him. Everything Vastra said was falling on deaf ears. He was in complete shock. He had caused all of this, he hadn't meant to, he'd just been trying to do the right thing but now people were dying for him. It was all his fault. Thinking about it he remembered their time in Florida. River had said the girl was human and strong but she might have just appeared that way.

"I see you accessed our files. Do you understand yet?" Madame Kovarian asked. "Oh, don't worry. I'm a long way away, but I like keeping tabs on you. The child, then, what do you think?"

"What is she?"

"Hope. Hope in this endless bitter war."

"What war? Against who?"

"Against you, Doctor."

"Daddy!" A little girl's voice called.

A jolt ran through him. One time, just that one time. Just after the Pit, the moment when they were still afraid, the prophecy, just before she was lost to him forever. It had been another life. There had been a trace of the Time War left in him and he'd still felt lost and alone. But then there was her, so bright, so alive, and he'd broken her in the end. She came back, just like she always did, and in order to protect them both he'd left her there again. He'd been trying to spare her any extra pain. Now, now he wished he'd dragged her with him, pregnant or not.

"Daddy, please!"the girl yelled again.

He couldn't see her but he could imagine her. So much like her mother, beautiful, bright and strong. "A child is not a weapon!" he yelled believing the voice was in his mind.

"Oh give us time, she can be, she will be." Kovarian said.

"Except you've already lost her, and, I swear, I will never let you anywhere near her again."

"Oh, Doctor. Fooling you once was a joy, but fooling you twice the same way- it's a privilege." she sneered.

It wasn't in his head. "If she's there..." _No..._His daughter, they had his daughter. "Listen to me, I will find you and when I do I'm going to bring you home. Do you hear me? I love you and I will find you."

"Good-bye, Doctor."

A rock dropped in his gut. The others were fighting for a fake child, they were dying for her. He ran. Tired and old, he ran for them. He reached the door screaming at them to stop, that the child was a fake. Once the door was finally open he rushed inside. The room was silent. He was too late to stop the fighting. Strax was down and Amy was curled up near a puddle of liquid flesh.

"Yeah, we know." Rory said slightly annoyed.

Suddenly everything was catching up to him. He had a daughter with Rose Tyler and now one was lost and the other was fighting off death. "She was my daughter." he said.

Amy looked up at him with wide green eyes. "What? But you said..."

"Yes, I did but I got it wrong." The doctor said burying his fingers in his hair. "It was one time, just once. I never though it was possible. If I had any clue I would have..."

The Doctor didn't have to say it, they knew. If he had known the child would never have been touched by anyone, ever. He would have made sure of that. There was no need to point out his mistakes, not with him kicking himself. Rose had never told him. She must have known on the beach but...she had said that Jackie was pregnant but...rule one...time travelers lie. But, why?! He didn't understand.

"So this was all for nothing, they took her anyway?" Amy said tears shining in her Doctor remained silent.

"Amy it's not his fault," Jenny said.

"I know, I know." She walked away sobbing. He didn't blame her. Her body had been tricked and she felt protective of the little girl who'd been held with her.

"Doctor," Vastra called. "There is someone who wants to speak to you." The Doctor turned and walked to her. "This is Lorna, she came to warn us."

He spoke kindly to her. He held her hand as she died. _I remember everyone. _Especially those who die or leave. A hollow pain pulsed through him breaking both his hearts anew. Yes he'd known her but not well, certainly not well enough to warrant this. She had died for him, for a child she didn't even know was his. A sob hit him hard. It took him a moment to regain the ability to speak.

"Who was she?"

"I don't know but she was very brave." Vastra said honestly.

"They're always brave."

The Doctor stood. Why were they always brave for him? Tremors passed through him as he thought of all those he'd lost, all those who'd been brave for him.

"So what now? They'd have almost certainly taken her to Earth, raise her in the correct environment."

"Yes, they did, and it's already to late."

"You're giving up? You never do that! She's your daughter."

"Yeah and don't you sometimes wish I did?"

There was a crash and flash of light signaling the use of an unattached vortex manipulator. Before all of them stood River Song with a bright smile. She'd come to gloat to rub salt into his already tender wounds.

"Well then soldier, how goes the day?" she asked still smiling.

"Where the hell have you been?! Every time you've asked I have been there. Where the hell were you today?!" The Doctor yelled.

"I couldn't have prevented this."

"You could have tried." He growled.

"And so could you." she said simply. "I know you're not alright but hold tight Amy because you will be."

"You think I wanted this? I didn't do this. This...This wasn't me!"

"This was exactly you. All this, all of it. You make them so afraid. When you began, all those years ago, sailing off to see the Universe, did you ever think you'd become this? The man who could turn an army around at the mention of his name. "Doctor," the word for healer and wise man through out the universe. We get that word from you, you know? But if you carry on the way you are, what might that word come to mean? To the people of the Gamma Forests, the word Doctor means might warrior. How far you've come. And now, they've taken a child, your child, and they're going to turn her into a weapon, just to bring you down. And all this, in fear of you."

"Who are you?"

"Oh the storm look, mum, told me about that." she said smile returning brighter than before as she danced out of his reach.

He grabbed her before she got too far away. "No, no, you tell me. You tell me who you are."

"I _am_ telling you. My mother called me River Song. When I was little she would whisper that my father's kind chose what they'd called themselves when they could their paths but until I did I was her little River. She said it was because the first and only time she was with my father was near a river on the forest moon of Shilrax 5. She told me that he whispered in her ear as they lay there and that it sounded more beautiful than any song she'd eve heard." She gave him a look like that alone would tell him who she was. When it didn't click she moved on.

"I was unexpected. According to him, my father couldn't have children but my mother loved me liked she'd planned for me her whole life. Whenever I asked my mother or Uncle John about him they would tell me he was a good man and if the could reach him, he would come to my side in an instant. My Uncle John tried to explain why my parents couldn't be together. There was something about the universe keeping them apart. He loved my mother very much and in some ways mum loved Uncle John back but never the way he wanted. So he stayed by her side and protected her, sometimes even from her own mind."

She looked back up as she stopped for a breath. When their eyes locked it was like she was begging the Doctor to know her. Sighing at the dumb look on his face she moved on.

"My grandmother told me John was exactly like my father in almost every way. She never liked my father but told me I was the best thing he'd ever done. At times John was my father figure. I helped me grow up and tutored me." she sighed again. "My mother had seen demons and knew they were coming for us. No one but John believed her. The three of us escaped the first attack. We started a new life far way, in a new world." She looked at Amy willing her to understand, _the little house in Florida. _"They killed John the second time and by the time they found us again my mother was a bear protecting her young. A woman in an eye patch took her away and locked her up to rot. They stole me and used my against those who never knew me for who I was."

The Doctor's jaw fell. "Your...Your..."

River nodded, eyes glistening. Before she could say more the Doctor wrapped her in a tight hug. He had a daughter named River Song, an archeologist, a Time Lady, and her mother's daughter. A smile spread across his face. He'd met his daughter long before e knew she'd been born. He'd found her a last. Rose needed to know. She needed to know that he found their daughter and that she grew up to be just like her, brave and clever and so much more. He pulled back.

"River, take them home would you?" the Doctor asked.

River nodded with a smile. He smiled back and negated the field surrounding the TARDIS. Hopping in he giggled with excitement. He needed to talk to Rose. More tan that he needed to hold her in his arms and explain every feeling he'd kept hidden sine the day they'd met. A rush of excitement tingled up his spine as he ran toward their room. Yes, it was theirs now, now and forever.

"Wait! Doctor! Who is she?! Amy yelled chasing after him. "Doctor!" she yelled just as the door shut in her face.

"Amy, listen. When I was just a little girl you fought for me. You kept me hoping when I thought I was truly lost." River stopped. "You told me they were coming for us."

"So your his and..." Amy said in shock.

River just smiled and nodded.


End file.
